org.bdgenomics.adam.rdd.variant
The underlying RDD of VariantContexts.
The genome sequence these variants were called against.
The genotyped samples in this RDD of VariantContexts.
The VCF header lines that cover all INFO/FORMAT fields needed to represent this RDD of VariantContexts.
Performs a broadcast inner join between this RDD and another RDD.
Performs a broadcast inner join between this RDD and another RDD.
In a broadcast join, the left RDD (this RDD) is collected to the driver, and broadcast to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other RDD are dropped.
The right RDD in the join.
Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.
Performs a broadcast inner join between this RDD and another RDD.
Performs a broadcast inner join between this RDD and another RDD.
In a broadcast join, the left RDD (this RDD) is collected to the driver, and broadcast to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other RDD are dropped.
The right RDD in the join.
Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.
Runs a filter that selects data in the underlying RDD that overlaps a single genomic region.
Runs a filter that selects data in the underlying RDD that overlaps a single genomic region.
The region to query for.
Returns a new GenomicRDD containing only data that overlaps the query region.
Runs a filter that selects data in the underlying RDD that overlaps several genomic regions.
Runs a filter that selects data in the underlying RDD that overlaps several genomic regions.
The regions to query for.
Returns a new GenomicRDD containing only data that overlaps the querys region.
Performs a sort-merge full outer join between this RDD and another RDD.
Performs a sort-merge full outer join between this RDD and another RDD.
In a sort-merge join, both RDDs are co-partitioned and sorted. The
partitions are then zipped, and we do a merge join on each partition.
The key equality function used for this join is the reference region
overlap function. Since this is a full outer join, if a value from either
RDD does not overlap any values in the other RDD, it will be paired with
a None in the product of the join.
The right RDD in the join.
Returns a new genomic RDD containing all pairs of keys that
overlapped in the genomic coordinate space, and values that did not
overlap will be paired with a None.
The variant context to get a reference region for.
Returns a seq containing the position key from the variant context.
The VCF header lines that cover all INFO/FORMAT fields needed to represent this RDD of VariantContexts.
The underlying RDD of genomic data, as a JavaRDD.
The underlying RDD of genomic data, as a JavaRDD.
Performs a sort-merge left outer join between this RDD and another RDD.
Performs a sort-merge left outer join between this RDD and another RDD.
In a sort-merge join, both RDDs are co-partitioned and sorted. The
partitions are then zipped, and we do a merge join on each partition.
The key equality function used for this join is the reference region
overlap function. Since this is a left outer join, all values in the
right RDD that do not overlap a value from the left RDD are dropped.
If a value from the left RDD does not overlap any values in the right
RDD, it will be paired with a None in the product of the join.
The right RDD in the join.
Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the left RDD that did not overlap a key in the right RDD.
Pipes genomic data to a subprocess that runs in parallel using Spark.
Pipes genomic data to a subprocess that runs in parallel using Spark.
Files are substituted in to the command with a $x syntax. E.g., to invoke a command that uses the first file from the files Seq, use $0.
Pipes require the presence of an InFormatterCompanion and an OutFormatter as implicit values. The InFormatterCompanion should be a singleton whose apply method builds an InFormatter given a specific type of GenomicRDD. The implicit InFormatterCompanion yields an InFormatter which is used to format the input to the pipe, and the implicit OutFormatter is used to parse the output from the pipe.
The type of the record created by the piped command.
A GenomicRDD containing X's.
The InFormatter to use for formatting the data being piped to the command.
Command to run.
Files to make locally available to the commands being run. Default is empty.
A map containing environment variable/value pairs to set in the environment for the newly created process. Default is empty.
Number of bases to flank each command invocation by.
Returns a new GenomicRDD of type Y.
The underlying RDD of VariantContexts.
The underlying RDD of VariantContexts.
The RDD of VariantContexts to replace the underlying RDD.
Returns a new VariantContextRDD where the underlying RDD has been replaced.
Performs a broadcast right outer join between this RDD and another RDD.
Performs a broadcast right outer join between this RDD and another RDD.
In a broadcast join, the left RDD (this RDD) is collected to the driver,
and broadcast to all the nodes in the cluster. The key equality function
used for this join is the reference region overlap function. Since this
is a right outer join, all values in the left RDD that do not overlap a
value from the right RDD are dropped. If a value from the right RDD does
not overlap any values in the left RDD, it will be paired with a None
in the product of the join.
The right RDD in the join.
Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right RDD that did not overlap a key in the left RDD.
Performs a broadcast right outer join between this RDD and another RDD.
Performs a broadcast right outer join between this RDD and another RDD.
In a broadcast join, the left RDD (this RDD) is collected to the driver,
and broadcast to all the nodes in the cluster. The key equality function
used for this join is the reference region overlap function. Since this
is a right outer join, all values in the left RDD that do not overlap a
value from the right RDD are dropped. If a value from the right RDD does
not overlap any values in the left RDD, it will be paired with a None
in the product of the join.
The right RDD in the join.
Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right RDD that did not overlap a key in the left RDD.
Performs a sort-merge right outer join between this RDD and another RDD.
Performs a sort-merge right outer join between this RDD and another RDD.
In a sort-merge join, both RDDs are co-partitioned and sorted. The
partitions are then zipped, and we do a merge join on each partition.
The key equality function used for this join is the reference region
overlap function. Since this is a right outer join, all values in the
left RDD that do not overlap a value from the right RDD are dropped.
If a value from the right RDD does not overlap any values in the left
RDD, it will be paired with a None in the product of the join.
The right RDD in the join.
Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right RDD that did not overlap a key in the left RDD.
Performs a sort-merge right outer join between this RDD and another RDD, followed by a groupBy on the left value, if not null.
Performs a sort-merge right outer join between this RDD and another RDD, followed by a groupBy on the left value, if not null.
In a sort-merge join, both RDDs are co-partitioned and sorted. The
partitions are then zipped, and we do a merge join on each partition.
The key equality function used for this join is the reference region
overlap function. In the same operation, we group all values by the left
item in the RDD. Since this is a right outer join, all values from the
right RDD who did not overlap a value from the left RDD are placed into
a length-1 Iterable with a None key.
The right RDD in the join.
Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, grouped together by the value they overlapped in the left RDD, and all values from the right RDD that did not overlap an item in the left RDD.
The genotyped samples in this RDD of VariantContexts.
The genotyped samples in this RDD of VariantContexts.
Converts an RDD of ADAM VariantContexts to HTSJDK VariantContexts and saves to disk as VCF.
Converts an RDD of ADAM VariantContexts to HTSJDK VariantContexts and saves to disk as VCF.
The filepath to save to.
If true, saves the output as a single file by merging the sharded output after completing the write to HDFS. If false, the output of this call will be written as shards, where each shard has a valid VCF header. Default is false.
The validation stringency to use when writing the VCF.
Converts an RDD of ADAM VariantContexts to HTSJDK VariantContexts and saves to disk as VCF.
Converts an RDD of ADAM VariantContexts to HTSJDK VariantContexts and saves to disk as VCF.
Whether to sort before saving.
The genome sequence these variants were called against.
The genome sequence these variants were called against.
Performs a sort-merge inner join between this RDD and another RDD.
Performs a sort-merge inner join between this RDD and another RDD.
In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other RDD are dropped.
The right RDD in the join.
Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.
Performs a sort-merge inner join between this RDD and another RDD, followed by a groupBy on the left value.
Performs a sort-merge inner join between this RDD and another RDD, followed by a groupBy on the left value.
In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other RDD are dropped. In the same operation, we group all values by the left item in the RDD.
The right RDD in the join.
Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, grouped together by the value they overlapped in the left RDD..
Sorts our genome aligned data by reference positions, with contigs ordered by index.
Sorts our genome aligned data by reference positions, with contigs ordered by index.
Returns a new RDD containing sorted data.
Does not support data that is unaligned or where objects align to multiple positions.
sortLexicographically
Sorts our genome aligned data by reference positions, with contigs ordered lexicographically.
Sorts our genome aligned data by reference positions, with contigs ordered lexicographically.
Returns a new RDD containing sorted data.
Does not support data that is unaligned or where objects align to multiple positions.
sort
Returns a GenotypeRDD containing the Genotypes in this RDD.
Returns the Variants in this RDD.
Applies a function that transforms the underlying RDD into a new RDD.
Applies a function that transforms the underlying RDD into a new RDD.
A function that transforms the underlying RDD.
A new RDD where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) is copied without modification.
An RDD containing VariantContexts attached to a reference and samples.
The underlying RDD of VariantContexts.
The genome sequence these variants were called against.
The genotyped samples in this RDD of VariantContexts.
The VCF header lines that cover all INFO/FORMAT fields needed to represent this RDD of VariantContexts.